Preprint Open Access

SARS-CoV-2 emergence very likely resulted from at least two zoonotic events

Pekar, Jonathan E.; Magee, Andrew; Parker, Edyth; Moshiri, Niema; Izhikevich, Katherine; Havens, Jennifer L.; Gangavarapu, Karthik; Malpica Serrano, Lorena M.; Crits-Christoph, Alexander; Matteson, Nathaniel L.; Zeller, Mark; Levy, Joshua I.; Wang, Jade C.; Hughes, Scott; Lee, Jungmin; Park, Heedo; Park, Man-Seong; Ching Zi Yan, Katherine; Tzer Pin Lin, Raymond; Mat Isa, Mohd Noor; Muhammad Noor, Yusuf; Vasylyeva, Tetyana I.; Garry, Robert F.; Holmes, Edward C.; Rambaut, Andrew; Suchard, Marc A.; Andersen, Kristian G.; Worobey, Michael; Wertheim, Joel O.


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    "description": "<p>Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversity prior to February 2020 comprised only two distinct viral lineages&mdash;denoted A and B&mdash;with no transitional haplotypes. Novel phylodynamic rooting methods, coupled with epidemic simulations, indicate that these two lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses and occurred in late-November/early-December 2019 and no earlier than the beginning of November 2019, while the introduction of lineage A likely occurred within weeks of the first event. These findings define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. Hence, as with SARS-CoV-1 in 2002 and 2003, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.</p>", 
    "language": "eng", 
    "title": "SARS-CoV-2 emergence very likely resulted from at least two zoonotic events", 
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    "keywords": [
      "SARS-CoV-2; zoonosis; phylodynamics; molecular clock"
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    "publication_date": "2022-02-26", 
    "creators": [
      {
        "affiliation": "Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.", 
        "name": "Pekar, Jonathan E."
      }, 
      {
        "affiliation": "Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.", 
        "name": "Magee, Andrew"
      }, 
      {
        "affiliation": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.", 
        "name": "Parker, Edyth"
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      {
        "affiliation": "Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.", 
        "name": "Moshiri, Niema"
      }, 
      {
        "affiliation": "Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.", 
        "name": "Izhikevich, Katherine"
      }, 
      {
        "affiliation": "Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.", 
        "name": "Havens, Jennifer L."
      }, 
      {
        "affiliation": "Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.", 
        "name": "Gangavarapu, Karthik"
      }, 
      {
        "affiliation": "Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.", 
        "name": "Malpica Serrano, Lorena M."
      }, 
      {
        "affiliation": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.", 
        "name": "Crits-Christoph, Alexander"
      }, 
      {
        "affiliation": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.", 
        "name": "Matteson, Nathaniel L."
      }, 
      {
        "affiliation": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.", 
        "name": "Zeller, Mark"
      }, 
      {
        "affiliation": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.", 
        "name": "Levy, Joshua I."
      }, 
      {
        "affiliation": "New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.", 
        "name": "Wang, Jade C."
      }, 
      {
        "affiliation": "New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.", 
        "name": "Hughes, Scott"
      }, 
      {
        "affiliation": "Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.", 
        "name": "Lee, Jungmin"
      }, 
      {
        "affiliation": "Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.", 
        "name": "Park, Heedo"
      }, 
      {
        "affiliation": "Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.", 
        "name": "Park, Man-Seong"
      }, 
      {
        "affiliation": "National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.", 
        "name": "Ching Zi Yan, Katherine"
      }, 
      {
        "affiliation": "National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.", 
        "name": "Tzer Pin Lin, Raymond"
      }, 
      {
        "affiliation": "Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.", 
        "name": "Mat Isa, Mohd Noor"
      }, 
      {
        "affiliation": "Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.", 
        "name": "Muhammad Noor, Yusuf"
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        "affiliation": "Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.", 
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        "name": "Garry, Robert F."
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        "affiliation": "Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.", 
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        "affiliation": "Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.", 
        "name": "Rambaut, Andrew"
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        "affiliation": "Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.", 
        "name": "Suchard, Marc A."
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        "affiliation": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.", 
        "name": "Andersen, Kristian G."
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        "affiliation": "Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.", 
        "name": "Worobey, Michael"
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        "affiliation": "Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.", 
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